Life – K from a nice volcanic mud puddle…

I’ve complained a few times in a few places about one of the Nagging Bits about cellular function that just doesn’t fit with the idea we evolved in the ocean on earth.

That is the fact that cells contain a LOT of K Potassium, and less Na Sodium, while the ocean has a lot of Na and not so much K.

“If we evolved in the ocean, why do our cells have pumps to keep the sodium out?”

I’d speculated that this could be evidence for panspermia, that maybe life originally evolved in some other cosmic ocean and got carried here. I’ve speculated it could even indicate Divine Intervention was useful in the getting started phase.

Then a comment on a WUWT article pointed me toward a Very Interesting Paper that has a tidy way of tying up the loose ends.

http://www.pnas.org/content/109/14/E821

Origin of first cells at terrestrial, anoxic geothermal fields

Armen Y. Mulkidjaniana,b,1, Andrew Yu. Bychkovc, Daria V. Dibrovaa,d, Michael Y. Galperine, and Eugene V. Koonine,1

Author Affiliations

Edited* by Norman H. Sleep, Stanford University, Stanford, CA, and approved January 17, 2012 (received for review October 28, 2011)

Abstract

All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the “hatcheries” of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate. Thus, protocells must have evolved in habitats with a high K+/Na+ ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO2-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K+, Zn2+, and phosphorous compounds.

There are some papers that just reek of unjustified leaps, or “given these conclusions what assumptions can we draw?”, or some are just sort of muddied untidy things. This paper is not one of them.

There are other papers that are somehow “just right”. Loose threads at the start, neatly tied off by the end. Things you’d not thought of, brought up and examined. A basic idea that expands what it explains with each paragraph, rather than creating more “issues” as you read. This is that kind of paper.

Not just K/Na ratio, but the excess phosphate, the large use of Zn in enzymes, and so much more. Neatly tied up in a self consistent and very reasonable package.

The full PDF is here: http://www.pnas.org/content/109/14/E821.full.pdf

Essentially, the authors looked at those same issues (like K/Na ratios and ion pumps), but also thought about why they would form, how life could evolve slowly bit by bit and only later add things like ion-tight membranes and ion pumps, how geology could make those conditions, and where. Then they connect all those dots into one nice picture.

Hit the link, read the PDF, bits quoted can’t do it justice.

But a couple of bits:

Origin of first cells at terrestrial, anoxic geothermal fields

Armen Y. Mulkidjanian a,b,1, Andrew Yu. Bychkov c, Daria V. Dibrova a,d, Michael Y. Galperin e, and Eugene V. Koonin e,1

a School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany;
b A. N. Belozersky Institute of Physico-Chemical Biology and Schools of
c Geology and
d Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia; and
e National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

Edited* by Norman H. Sleep, Stanford University, Stanford, CA, and approved January 17, 2012 (received for review October 28, 2011)
[…]

For example, ancient, ubiquitous proteins often use Zn and Mn, but not Fe, as transition metal cofactors; this preference is retained across the three domains of life (12). The abundance of Zn- and Mn-dependent enzymes during the earliest steps of evolution and the later recruitment of Fe has been inferred also from a global phylogenomic re-construction (13). The prevalence of Zn-dependent ancestral enzymes is particularly remarkable given the low estimated concentration of Zn in the anoxic ocean of 10^−12 to 10^−16 M (14,15) and indicates that the first organisms might have dwelled inspecific, Zn-enriched habitats (12, 16). Here we combine geochemical evidence with the data on the overall ionic composition of the modern cells, with a particular emphasis on their universal preference for K+ ions over Na+ ions. Geochemical analysis shows that, contrary to the common belief that associates the origin of life with marine environments, the first cells could have emerged at inland geothermal fields within ponds of condensed and cooled geothermal vapor.
[…]

It goes on from there. Showing why ocean origin can’t work (some enzymes that are essential can’t form or function with that much Na) and then on to look at geothermal fields, how they sort and stratify minerals, how with an atmosphere missing oxygen, they would make amines and even oils and RNA. Every thread that needs pulling gets pulled, and explained.

I was particularly fond of this bit, not for the origin of life angle, but for how nicely they cover formation of hydrocarbons. Life runs on oil. Cell membranes are lipid layers. So perhaps this also explains some of how abiotic oil can form? Bold mine.

The absence of any enzymes related to autotrophy in the ubiquitous protein set (SI Appendix, Table S1) suggests that the protocells were heterotrophs, i.e., their growth depended on the supply of abiotically produced organic compounds (32, 75–77). At least two continuous, abiotic sources of such compounds would exist in the described geothermal systems. First, even in modern vapor-dominated geothermal systems, exhalations carry organic molecules that are believed to be formed, at least partly, in the process of hydrothermal alteration of ultramafic rocks (78,79). Hydrothermal alteration occurs when iron-containing rocks interact with water at temperatures of approximately 300 °C, which is typical of terrestrial geothermal systems. Under these conditions, part of the Fe 2+ in the rock is oxidized to Fe3+, yielding magnetite (Fe3O4). The electrons released through this reaction are accepted by protons of water yielding H2; in the presence of water-dissolved CO2, diverse hydrocarbons are ultimately produced (78). It could be argued that the hydrothermal rock alteration might also account for the reduction of insoluble apatite to soluble phosphite (47), explaining the presence of phosphite in the geothermal fluids (56). Similar reactions couldlead to the ammonia formation (80), which might account for the high ammonia content in the exhalations of geothermal fields [as much as 130 mg/L in the mud pot solutions of Kamchatka (55)]. In addition, diverse organic molecules could be produced by abiotic photosynthesis catalyzed by ZnS and MnS particles (81–84). Such crystals are semiconductors, which can trap quanta with a λ of less than 320 nm and transiently store their energy in a form of charge-separated states, capable of reducing diverse compounds at the surface (81). Thereby, crystals of ZnS are the most powerful photocatalysts known in nature (10).‡ Particles of ZnS can catalyze photopolymerization reactions (85) and photo reduce carbonaceous compounds to diverse organic molecules, including intermediates of the tricarboxylic acid cycle (83, 84); the highest quantum yield of 80% was observed upon reduction of CO2 to formate (81).

So the paper is kind of a ‘two fer’. Pointers on abiotic oil and hydrocarbons, and an answer to why life is like it is. I’d only add that the general thought process most folks use, starts with our present cellular life and asks “How can this evolve all at once?”. Suddenly getting both RNA and DNA replication going and getting needed machinery like membrane ion pumps to evolve and install to let it all run. This paper solves some of the chemical issues.

My idea is that in such a puddle of chemicals, the whole puddle can be one living thing, only later dividing up into cells with control of ions at the membrane. Look at some of the slime molds. They can break up or not, and have many different nuclear areas inside one giant ‘cell’. I’d envision a large puddle of RNA, hydrocarbons (fats) and such. Slowly making RNA replicators and very leaky membranes (since the environment is essentially making cytoplasm, you don’t really want to keep it out). Only later breaking up into droplets with “cell walls” and adding ion pumps over a very long period of time. As those lumps with better internal control replicate more and die off less in the rain (or a seawater splash…)

This lets many bits of interior mechanism develop over a very long time ( RNA replication, fat metabolism, Citric Acid Cycle) only later working out how to make a nucleus and cell walls, and finally adding ion pumps to less leaky cell walls. At that point, cellular life as we know it can take over the world….

If the entire pond is the first life, then evolving bits slowly, and gradually approaching “final assembly” is much easier to have happen. The only hard bit is having that puddle make those bits. This article explains how that happens.

I’m pretty sure that those two things in conjunction explains how life can start.

For folks of a creationist bent: My standard way to resolve that with “Science” is simply to ask a question: Could this not be the method by which God created life? I see the study of chemistry, physics, biology, etc. as the study of the methods of the universe, and religion as the study of the meaning. Knowing the methods used does not change the meaning of creation… and personally I find the idea of creating a chemical system that self assembles into life a far more interesting act of creation. When I go looking for a file on my computer, I don’t open each file by hand; I write a bit of instructions to do the looking automatically. I’d expect a creator God to have at least that good a programming skill too… and I find the idea of me putting limits on how a God can work to be a bit cheeky.

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About E.M.Smith

A technical managerial sort interested in things from Stonehenge to computer science. My present "hot buttons' are the mythology of Climate Change and ancient metrology; but things change...
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30 Responses to Life – K from a nice volcanic mud puddle…

  1. philjourdan says:

    Food for thought. Or, how science is supposed to work. If you recall in STNG, the origin of life was a puddle at the edge of a volcano. A primordial “goo”. So maybe that idea has been around for a lot longer and Roddenberry just picked up on it.

  2. H.R. says:

    I see the study of chemistry, physics, biology, etc. as the study of the methods of the universe, and religion as the study of the meaning. Knowing the methods used does not change the meaning of creation… and personally I find the idea of creating a chemical system that self assembles into life a far more interesting act of creation.

    That’s a nice tidy way to distinguish between religion and science, E.M. Monotheism always made more sense to me than pantheism. Design by committee rarely, if ever, works out. Heaven help us if God turns out to be the Creative Division of some multi-universe bureaucracy.

    This paper makes a good case for how life could have started on Earth. But has anyone been able to imagine other paths to life on planets that are not Earth-like? I’ve read speculations of silica-based life tromping around on some planet, but why couldn’t life exist in a gaseous environment? Think of a planet where stringy beings float around in the gaseous atmosphere; atmospheric jellyfish.

    Anyhow, good find. Thank you. I’m going to have to hit the .pdf later. I retired this year so I have time to read more and comment a bit more, and that is (Martha Stewart voice) “a good thing.”

  3. catweazle666 says:

    “I’d expect a creator God to have at least that good a programming skill too”

    Yes, I have often pondered over the astonishing beauty and elegance of the double spiral, and how it permits any possible carbon-based life form to be precisely described, but at the same time is very amenable to programatic modification so as to to be adaptable to almost any environmental niche, voila Darwinian evolution, from a butterfly to a sperm whale. I have great difficulty envisaging how such an elegant solution could come about by the random association of a mixture of atoms in some primeval soup.

    Remarkable also that now we, the human race, have cracked that code and are in a position to design and build literally any carbon based organism that can possibly exist…

  4. Gail Combs says:

    Yes, Agreed EM I see not inconsistency between science and religion. After all there are ‘laws’

    On a different note Ice Age Now had a pointer to an interesting story and vid along the same lines.

    Shrimp with eyes on their backs at hydrothermal vents The water at underwater hot springs is hot enough to melt lead, and yet, life not only survives, it thrives.

  5. PaulID says:

    just look at DNA it is at it’s root a self replicating binary code software that creates the hardware that is runs on God is without a doubt a coder and he has a great sense of humor also.

  6. David Ball says:

    Really enjoying hanging out here.

  7. Gail Combs says:

    David, glad you joined our merry band.

    With E.M.’s curiosity and ‘Dig Here’ style, things get interesting.

  8. pg sharrow says:

    The muds of a geothermal vent are much more conducive to the origin of life then the tidal flats of a brakish ocean. Ocean waters represent the lowest energy potential within it’s chemistry, while the minerials of a geothermal vent have a great deal of energy potential to release into the enviroment. Colonization of the oceans could come later as the energies of sunlight could be add into the “stew” and the oceanic salts act as fertilizer for the multiplying life…pg

  9. rocketplumber says:

    Interesting that it turns upside down the old paradigm of life orginating in the ocean and only later colonizing the land, to life starting inland and only later colonizing the sea… On reading the paper i agree that it all hangs together remarkably well, even invoking the anoxic conditions as the reason the vents were _not_ acidic back then, since H2S did not oxidize to make sulfuric acid. I get a very strong feeling of “this all makes sense” from the paper. A hundred years from now it may be as famous as Darwin’s Origin of Species.

  10. E.M.Smith says:

    @Rocketplumber:

    Neat feeling, isn’t it :-)

    @P.G.:

    Interesting point about the energetics of the ocean already being run down… Volcanics give the quick and easy chemical energy path to metabolism, machinery added later then final packaging in cell walls…

    @David Ball & Gail:

    Glad you like it… I just ask questions that interest me and let folks talk about it in relative peace. (Tossing rocks at each other is about the only thing I suppress…)

    Turns out, that looks like enough…

    @PaulId:

    I first thought proteins were key. Later I came to see DNA as key, then realized RNA was first and more key… Now I’m realizing it is an ionic soup and RNA that is THE key trick…

    Now the fun bit is speculating if RNA and a different rock soup with different mineral mix could lead to a different basic life chemistry. Maybe like that arsenic tolerant bacteria. Make the soup with arsenic instead of phosphorus and sodium instead of potassium then cadmium instead of zinc. Each close to the original chemistry. Could the proteins evolve enough differently for life to still form? I’d bet so…

    That leads to some very interesting expectations about life on other planets… starting from other rocks…

  11. cdquarles says:

    Sure, this could be the method God created (in potentia) then made actual. God Is Existence, whole, being Cause itself. There is no mother nature, there is Father God. You can fool nature, in a sense; but you can’t fool God.

  12. Larry Ledwick says:

    Item on evidence of early life dated at 3.7 billion years ago
    http://bigstory.ap.org/f8406b09b59946d9a4a95ecc768dd757

  13. E.M.Smith says:

    @Larry:

    That is one of THE biggest problems with the present evolution based story of the start of life. You don’t have billions of years for it. Just millions. Still a long time, but… then you must deduct for cooling time after the late heavy bombardment…

    The only two viable options are seeding from space, or VERY rapid evolution from rocks and water to life…

  14. Larry Ledwick says:

    I would posit one other possibility, and that would be that the chemistry of early earth is such that it “must” produce RNA etc. If you mix hydrogen and oxygen and provide some energy input above ignition threshold, it “must” form water. I suspect building blocks of life are much the same. They have done multiple simulations of what happens when space dust/gasses are exposed to strong UV and radiation, and the experiments demonstrate that it invariably forms many if not all the essential precursor chemicals of life. In that sense seeding is already proven.

    If the same sort of studies in geothermal vent conditions spontaneously produces primitive essential chemicals for life and chemical potentials for bonding and any necessary catalysts are pressent so that it assembles sufficiently complex protein strings to initiate self replication with energy input, then life is essentially inevitable and required with appropriate chemistry under the physical laws of your universe.

    I see no difference in the miracle of creation regardless of how the physical process proceeds or how long it takes in our concept of time.

  15. Gail Combs says:

    My organic chemistry is way too old and long ago but carbon likes to react and gloms on to hydrogen and oxygen.
    Straight carbon (coal) burns readily and forms CO2 although that would be after life had formed and the atmosphere had free O2.

    Reactions Between Elemental Carbon and Hydrogen at High Temperatures (like in volcanoes)
    http://pubs.acs.org/doi/abs/10.1021/i260003a003

    Carbon reacts with H at 800K
    C(solid) + H2 (gas) ==> CH2

    At 2500K
    2C + H2 ==> C2H2

    At that point (C2H2) add catalysts and other elements and off you go.

    We also know that sunlight and lightening gives us NOx in the atmosphere very easily.

    C, H, O and N are the basic elements of life with a dash of several others like K, Na, Fe and even arsenic.

  16. pg sharrow says:

    Digging and boring deeply into the crust of the Earth has reveled living organisims to great depth. There is many times the mass of life on the surface dwelling with in the crust of the Earth. The “organic” chemistry of carbonacious material takes place everywhere that energy levels permit. “Life” seems to be inevitable. Complex organized life may require special conditions to evolve…pg

  17. Gail Combs says:

    I posted this up thread but it belongs here too.
    Shrimp with eyes on their backs at hydrothermal vents – Video

    The water at underwater hot springs is hot enough to melt lead, and yet, life not only survives, it thrives.

    VIDEO

    Huge red-tipped tube worms, ghostly fish, strange shrimp with eyes on their backs and other unique species thrive near undersea hydrothermal vents.

    The vents spew toxic chemicals.

    For these animals, the key is chemosynthesis – they get their energy from chemicals.

    http://ocean.si.edu/ocean-videos/hydrothermal-vent-creatures

  18. Gail Combs says:

    MORE, (I am trying to find the actual temperature. — “A Black Smoker is an oceanic ridge vent which produces a plume of hydrothermal fluids with black sulphide particles. It is a type of undersea solfatara. Temperatures are usually > 330 deg C.” — (wwwDOT)volcanolive.com/blacksmoker.html )

    …Beneath the Caribbean Sea a remotely controlled vehicle came upon the world’s deepest hydrothermal vents, where super-heated mineral-rich water gushes from chimney structures onto the ocean floor.

    The black smokers, named for how they spew out an iron sulfide compound that’s black, sit 3.1 miles (5 kilometers) deep in the Cayman Trough in the Caribbean. While black smokers are the hottest of the undersea vents, white smokers are cooler and often contain compounds that are white in color.

    Until now, the deepest known vents had been found some 2.6 miles (4.2 km) below the sea surface….

    It might seem the scorching water spouting from the vents would be a “danger” sign to any life forms.

    But it turns out alien-like creatures that can withstand the heat and suffocating pressure thrive there. For instance, vents in the Pacific Ocean are known to teem with tubeworms and giant clams, while the Atlantic variety is typically home to eyeless shrimp and other extreme residents….
    http://www.livescience.com/8188-world-deepest-undersea-vents-discovered.html

    Black Smokers: Incubators on the Seafloor (6 pages)

    Perhaps the most far-reaching idea to come from these hot springs is that life itself may have originated within these dynamic systems, in which geological, chemical, and biological processes are intimately linked.

    …The exact physical and chemical processes by which hydrothermal vents begin to develop are still poorly understood. In young hydrothermal systems, plumes of hot water that rise through the crust beneath the seafloor have to displace the surrounding cooler seawater saturating the shallow portions of the oceanic crust. In order for the high-temperature fluids to reach the seafloor, the channels through which this water rises must become progressively insulated by deposition of minerals. Once a venting system is established, however, the black smokers grow and evolve as the high temperature fluids vent onto the seafloor. The metal-rich fluids, heated to 350–400°C, mix turbulently with oxygen-rich, cold (2°C) seawater. This drastic temperature change causes solids to precipitate from the fluid. This process generates particles of sulfide minerals such as pyrite, chalcopyrite, and sphalerite, and sulfates such as anhydrite and barite….

  19. E.M.Smith says:

    The black smoker origin thesis is aided by the fact that temp cycling is how you replicate DNA and RNA. The water swirling near smokers can take dozens of cycles an hour.

    The land thesis now has the advantage of the right chemical mix (but only one daily temp cycle and not as wide a range).

    I suspect reality may have been where an ocean ridge came ashore. Somewhere like Iceland today…

  20. Gail Combs says:

    E.M. wouldn’t the area near a black smoker in a shallow sea 3 to 4 billion years ago have the right chemical mix?

    The seas then certainly would be nothing like today.

  21. E.M.Smith says:

    Good point… Pangea near breakup had lots of shallow seas…

  22. Gail Combs says:

    Large shallow soup bowls full of chemicals with a lot of volcanic activity as the earth cooled.

    Sounds like the recipe for developing life.

  23. Larry Ledwick says:

    Another good candidate is emerging volcanic islands and the surf zone surrounding them, similar to ocean ridge emergence like iceland noted above, but also pacific volcanic islands like Hawaii and the south pacific ring of fire islands have huge shore line lengths. Deep ocean ridges are pretty steady state where as emerging islands and similar is constantly providing new and interesting variations.

    This was the niche that I understand created the Cyanobacteria blooms and our atmospheric oxygen, and perhaps aquatic organisms which benefited from free oxygen and or diminished iron concentrations as the free oxygen purged the ocean of iron by precipitation.

    Good mixing, good temperature contrasts (so for any critical temperature niche somewhere in that zone it exists). Lots of physical pulverization of the rock and “oxygenation” or what ever the local atmosphere was rich in at that point in time, to get reactions working. Enormous surface area in the sands (for things that need foot holds to develop from)

  24. Gail Combs says:

    I think the key is water (as solvent) plus volcanic action for heat and reactants.

  25. cdquarles says:

    Exactly, for we are talking water-shift or Fischer-Tropsch pyrolysis type redox reactions. Here: http://www.fischer-tropsch.org/

  26. Gail Combs says:

    From WIKI “…A Fischer–Tropsch-type process has also been suggested to have produced a few of the building blocks of DNA and RNA within asteroids.[2]…”

    2. Pearce, Ben K. D.; Pudritz, Ralph E. (2015). “Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways”. ApJ. 807: 85. doi:10.1088/0004-637X/807/1/85.

    More links at WIKI

    (Dang, I keep trying to forget all the chemistry I learned in college and at work….)

  27. E.M.Smith says:

    Tee Heee…

    Surprizing how hard it is to forget useful things… :-)

    I’d say we’re narrowing in on the process details…

  28. Gail Combs says:

    The one impression that managed to stick is that chemistry is like farming. Provide the right feed stocks, temperature, pressure and catalysts and then stand back and watch nature take over and hope you don’t blow the darn place up. (And yes we did blow the place up on occasion.)

  29. Pingback: Please Pass The Arsenic… | Musings from the Chiefio

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